Conformational isomerism

About: Conformational isomerism is a(n) research topic. Over the lifetime, 11563 publication(s) have been published within this topic receiving 199312 citation(s).

Circular dichroism and conformational polymorphism of DNA

Abstract: Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.

Novel Cavity Design Using Calix[n]arene Skeletons: Toward Molecular Recognition and Metal Binding.

Abstract: Calixarenes are macrocyclic molecules, like crown ethers and cyclodextrins.1-7 Calixarenes made up of phenol and methylene units have many conformational isomers because of two possible rotational modes of the phenol unit: the oxygen-through-theannulus rotation and the para-substituent-throughthe-annulus rotation (Figure 1). The conformational isomers thus yielded afford a great number of unique cavities with the different size and the different shape. Recently, a number of strategies have been exploited by which not only the conformation of calix[4]arenes, but also those of calix[6]arenes and calix[8]arenes, can be immobilized. This means that our group can now design various calixarene-based receptors that show high selectivity for guest molecules and metal cations. In this review article, our group describe novel strategies for cavity design using calix[n]arene skeletons, strategies that are intended to allow complexation of specific molecular targets or metal ions.

An internal-coordinate Monte Carlo method for searching conformational space

Abstract: An internal coordinate, random-search method for finding the low-energy conformations of organic molecules is described. The search is biased toward the low-energy regions of conformational space by choosing starting geometries for each step in the conformational search from among previously stored low-energy conformers. Tendencies of the search method to concentrate in certain regions of conformational space at the expense of others are reduced by uniform usage of stored structures as starting geometries and by using varying numbers or torsional rotations in each step. Tests of the procedure's ability to find all low-energy conformations of several acrylic, medium- and large-ring molecules are described. Direct comparisons of the method with Cartesian coordinate random methods and systematic internal coordinate grid searches are carried out with symmetrical and unsymmetrical molecules. The method makes it possible to carry out global conformational searches on symmetrical and unsymmetrical molecules having up to a dozen variable torsion angles.

Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer

Abstract: Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.

Stereochemical Determination of Acyclic Structures Based on Carbon−Proton Spin-Coupling Constants. A Method of Configuration Analysis for Natural Products

Abstract: A method for elucidating the relative configuration of acyclic organic compounds was developed on the basis of carbon-proton spin-coupling constants ((2,3)J(C,H)) and interproton spin-coupling constants ((3)J(H,H)). This method is based on the theory that, in acyclic systems, the conformation of adjacent asymmetric centers is represented by staggered rotamers, and their relative stereochemistry can be determined using (2,3)J(C,H) and (3)J(H,H), because the combined use of these J values enables the identification of the predominant staggered rotamer(s) out of the six possible derived from threo and erythro configurations. Detailed conformational analysis for model compounds 1-4 revealed that this method is useful in most cases for assignment of the configuration of acyclic structures occurring in natural products, in which stereogenic methine carbons are often substituted with a methyl or a hydroxy (alkoxy) group. This J-based configuration analysis was applied to the stereochemical elucidation of carboxylic acid 5 derived from zooxanthellatoxin and proven to be a practical method even for natural products with complicated structures.